PL EN


Preferencje help
Widoczny [Schowaj] Abstrakt
Liczba wyników
2015 | 64 | 1 |

Tytuł artykułu

Effect of DNA extraction methods on the apparent structure of yak rumen microbial communities as revealed by 16S rDNA sequencing

Warianty tytułu

Języki publikacji

EN

Abstrakty

EN
To more efficiently identify the microbial community of the yak rumen, the standardization of DNA extraction is key to ensure fidelity while studying environmental microbial communities. In this study, we systematically compared the efficiency of several extraction methods based on DNA yield, purity, and 16S rDNA sequencing to determine the optimal DNA extraction methods whose DNA products reflect complete bacterial communities. The results indicate that method 6 (hexadecyltrimethylammomium bromide-lysozyme-physical lysis by bead beating) is recommended for the DNA isolation of the rumen microbial community due to its high yield, operational taxonomic unit, bacterial diversity, and excellent cell-breaking capability. The results also indicate that the bead-beating step is necessary to effectively break down the cell walls of all of the microbes, especially Gram-positive bacteria. Another aim of this study was to preliminarily analyze the bacterial community via 16S rDNA sequencing. The microbial community spanned approximately 21 phyla, 35 classes, 75 families, and 112 genera. A comparative analysis showed some variations in the microbial community between yaks and cattle that may be attributed to diet and environmental differences. Interestingly, numerous uncultured or unclassified bacteria were found in yak rumen, suggesting that further research is required to determine the specific functional and ecological roles of these bacteria in yak rumen. In summary, the investigation of the optimal DNA extraction methods and the preliminary evaluation of the bacterial community composition of yak rumen support further identification of the specificity of the rumen microbial community in yak and the discovery of distinct gene resources.

Słowa kluczowe

Wydawca

-

Rocznik

Tom

64

Numer

1

Opis fizyczny

p.29-36,fig.,ref.

Twórcy

autor
  • College of Life Science and Technology, Southwest University for Nationalities, Chengdu, Sichuan, PR China
autor
  • Institute of Qinghai-Tibetan Plateau, Southwest University for Nationalities, Chengdu, Sichuan, PR China
autor
  • College of Life Science and Technology, Southwest University for Nationalities, Chengdu, Sichuan, PR China
autor
  • College of Life Science and Technology, Southwest University for Nationalities, Chengdu, Sichuan, PR China
autor
  • Institute of Qinghai-Tibetan Plateau, Southwest University for Nationalities, Chengdu, Sichuan, PR China

Bibliografia

  • An D., X. Dong and Z. Dong. 2005. Prokaryote diversity in the rumen of yak (Bos grunniens) and Jinnan cattle (Bos taurus) estimated by 16S rDNA homology analyses. Anaerobe. 11: 207–215.
  • Bergmann I., K. Mundt, M. Sontag, I. Baumstark, E. Nettmann and M. Klocke. 2010. Influence of DNA isolation on Q-PCR-based quantification of methanogenic Archaea in biogas fermenters. Syst. Appl. Microbiol. 33: 78–84.
  • Bibby K., E. Viau and J. Peccia. 2010. Pyrosequencing of the 16S rRNA gene to reveal bacterial pathogen diversity in biosolids. Water. Res. 44: 4252–4260.
  • Colwell R.K. and J.A. Coddington. 1994. Estimating terrestrial biodiversity through extrapolation. Philos. Trans. R. Soc. Lond. B. Bio. Sci. 345: 101–118.
  • Cuív P.Ó., D.A. Cárcer, M. Jones, E.S. Klaassens, D.L. Worthley, V.L. Whitehall, S. Kang, C.S. McSweeney B.A. Leggett and M. Morrison. 2011. The effects from DNA extraction methods on the evaluation of microbial diversity associated with human colonic tissue. Microb. Ecol. 61: 353–362.
  • Fouts D.E., S. Szpakowski, J. Purushe, M. Torralba, R.C. Waterman, M.D. MacNeil, L.J. Alexander and K. E. Nelson. 2012. Next generation sequencing to define prokaryotic and fungal diversity in the bovine rumen. PLoS One. 7: e48289.
  • Gotelli N.J. 2002. Ecology: Biodiversity in the scales. Nature 419: 575–576.
  • Guan L.L., J.D. Nkrumah, J.A. Basarab and S.S. Moore. 2008. Linkage of microbial ecology to phenotype: correlation of rumen microbial ecology to cattle’s feed efficiency. FEMS Microbiol. Lett. 288: 85–91.
  • Guo F. and T. Zhang. 2013. Biases during DNA extraction of activated sludge samples revealed by high throughput sequencing. Appl. Microbiol. Biotechnol. 97: 4607–4616.
  • Henderson G., F. Cox, S. Kittelmann, V.H. Miri, M. Zethof, S.J. Noel, G.C. Waghorn and P.H. Janssen. 2013. Effect of DNA Extraction methods and sampling techniques on the apparent structure of cow and sheep sumen microbial communities. PLoS One. 8: e74787.
  • Huang X.D., H.Y. Tan, R.J. Long, J.B. Liang and A.D. Wright. 2012. Comparison of methanogen diversity of yak (Bos grunniens) and cattle (Bos taurus) from the Qinghai-Tibetan plateau, China. BMC Microbiol. 12: 237.
  • Jami E. and I. Mizrahi. 2012. Composition and similarity of bovine rumen microbiota across individual animals. PLoS One. 7: e33306.
  • McOrist A.L., M. Jackson and A.R. Bird. 2002. A comparison of five methods for extraction of bacterial DNA from human faecal samples. J. Microbiol. Methods. 50: 131–139.
  • Nettmann E., I. Bergmann, K. Mundt, B. Linke and M. Klocke. 2008. Archaea diversity within a commercial biogas plant utilizing herbal biomass determined by 16S rDNA and mcrA analysis. J. Appl. Microbiol. 105: 1835–1850.
  • Omoniyi L.A., K.A. Jewell, O.A. Isah, A.P. Neumann, C.F. Onwuka, O.M. Onagbesan and Suen G. 2014. An analysis of the ruminal bacterial microbiota in West African Dwarf sheep fed grass and tree-based diets. J. Appl. Microbiol. 116: 1094–1105.
  • Petri R.M., T. Schwaiger, G.B. Penner, K.A. Beauchemin, R.J. Forster, J.J. McKinnon and T.A. McAllister. 2013. Characterization of the core rumen microbiome in cattle during transition from forage to concentrate as well as during and after an acidotic challenge. PLoS One. 8: e83424.
  • Qiu Q., G. Zhang, T. Ma, W. Qian, J.Wang, Z. Ye, C. Cao, Q. Hu, J. Kim and D.M. Larkin. 2012. The yak genome and adaptation to life at high altitude. Nature. Genet. 44: 946–949.
  • Ross E.M, P.J Moate, C.R. Bath, S.E. Davidson, T.I. Sawbridge, M. Guthridge, B.G. Cocks and B.J. Hayes. 2012. High throughput whole rumen metagenome profiling using untargeted massively parallel sequencing. BMC Genet. 13: 53.
  • Schloss P.D. and J. Handelsman. 2005. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl. Environ. Microbiol. 71: 1501–1506.
  • Turnbaugh P. J., F. Bäckhed, L. Fulton and J.I. Gordon. 2008. Dietinduced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell. Host. Microbe. 3: 213–223.
  • Villegas-Rivera G., Y. Vargas-Cabrera, N. González-Silva, F. Aguilera-García, E. Gutiérrez-Vázquez, A. Bravo-Patiño, M. CajeroJuárez, V.M. Baizabal-Aguirre and J.J. Valdez-Alarcón. 2013. Evaluation of DNA extraction methods of rumen microbial populations. World. J. Microbiol. Biotechnol. 29: 301–307.
  • Willner D., J. Daly, D. Whiley, K. Grimwood, C.E. Wainwright and P. Hugenholtz. 2012. Comparison of DNA extraction methods for microbial community profiling with an application to pediatric bronchoalveolar lavage samples. PLoS One. 7: e34605.
  • Yu Z. and M. Morrison. 2004. Improved extraction of PCR-quality community DNA from digesta and fecal samples. Biotechniques. 36: 808–813.
  • Zened A., S. Combes, L. Cauquil, J. Mariette, C. Klopp, O. Bouchez, A. Troegeler-Meynadier and F. Enjalbert. 2013. Microbial ecology of the rumen evaluated by 454 GS FLX pyrosequencing is affected by starch and oil supplementation of diets. FEMS Microbiol. Ecol. 83: 504–514.
  • Zhang T., M.F. Shao and L. Ye. 2012. 454 Pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treatment plants. ISME, J. 6: 1137–1147.
  • Zhou M., E. Hernandez-Sanabria and L.L. Guan. 2009. Assessment of the microbial ecology of ruminal methanogens in cattle with different feed efficiencies. Appl. Environ. Microbiol. 75: 6524–6533.

Typ dokumentu

Bibliografia

Identyfikatory

Identyfikator YADDA

bwmeta1.element.agro-0155026a-ea17-4677-bff1-c7ce04ba938c
JavaScript jest wyłączony w Twojej przeglądarce internetowej. Włącz go, a następnie odśwież stronę, aby móc w pełni z niej korzystać.